title: Unexpected features in the Protein Data Bank entries 3qd1 and 4i8e: the structural description of the binding of the serine-rich repeat adhesin GspB to host cell carbohydrate receptor is not a solved issue.
abstract: The structure of a complex between a fragment of the adhesin GspB from Streptococcus gordonii and a disaccharide (PDB entries 3qd1 and 4i8e) has recently been proposed to identify the binding site for the sialyl-T antigen recognized by GspB. This structure exhibits numerous unrealistic and unusual features such as an excessive number of van der Waals clashes and a lack of correlation between atomic structure and experimental electron density. Here, it is shown that the crystallographic data can be fully explained by an alternative model, namely replacing the disaccharide with a buffer molecule. The conclusion is that the experimental data are likely to contain no information regarding the carbohydrate receptor binding site in GspB or the interaction of GspB with host cell receptors.
authors.affiliation: Lehrstuhl für Biotechnik, Department of Biology, Friedrich-Alexander University Erlangen-Nuremberg, Henkestrasse 91, 91052 Erlangen, Germany.
authors.forename: Yves A
authors.initials: YA
authors.lastname: Muller
mesh_terms: D018829:Adhesins, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D002241:Carbohydrates / Q000737:chemistry*; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D011956:Receptors, Cell Surface / Q000378:metabolism*; D020449:Repetitive Sequences, Amino Acid; D012694:Serine; D055672:Static Electricity; D054773:Streptococcus gordonii / Q000378:metabolism
chemical_list: D018829:Adhesins, Bacterial; D002241:Carbohydrates; D008024:Ligands; D011956:Receptors, Cell Surface; D012694:Serine
keywords: adhesion; misleading ligand identification; model error; pathogen–host cell recognition